Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001064.1 Hibiscus syriacus cultivar Beakdansim tig00002104_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 86231
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:5076 original size:37 final size:37
Alignment explanation
Indices: 5032--5106 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 37
5022 TTTATCAATC
* *
5032 TCCATTCTCCATGCTTGAAACGTCACCTTCTAATCTT
1 TCCATTCTCCATGCCTAAAACGTCACCTTCTAATCTT
* * *
5069 TCCATTCTCCATGCCTAAAAGGTTATCTTCTAATCTT
1 TCCATTCTCCATGCCTAAAACGTCACCTTCTAATCTT
5106 T
1 T
5107 GATTATGATT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.23, C:0.29, G:0.08, T:0.40
Consensus pattern (37 bp):
TCCATTCTCCATGCCTAAAACGTCACCTTCTAATCTT
Found at i:5285 original size:45 final size:45
Alignment explanation
Indices: 5210--5307 Score: 135
Period size: 45 Copynumber: 2.2 Consensus size: 45
5200 TAACATAGCT
* * *
5210 AAATTTCATGAATGAAACTCCATTTTCATTTTCATTTCCATTTCC
1 AAATTTCATGAATGAAACTCCATTTCCATTTCCATTCCCATTTCC
*
5255 AAATTTCATGAATGAAAC-CCAATTTCCATTTCCATTCCCATTTGC
1 AAATTTCATGAATGAAACTCC-ATTTCCATTTCCATTCCCATTTCC
*
5300 AATTTTCA
1 AAATTTCA
5308 ATTTTCATGT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 2 0.04
45 45 0.96
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.41
Consensus pattern (45 bp):
AAATTTCATGAATGAAACTCCATTTCCATTTCCATTCCCATTTCC
Found at i:10927 original size:20 final size:19
Alignment explanation
Indices: 10898--10950 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
10888 TTATTCAATG
* *
10898 GGTATTGATACTGTAGGTGA
1 GGTATCGATACTGCAGG-GA
*
10918 GGTATCGATACTCGCAGGGT
1 GGTATCGATACT-GCAGGGA
10938 GGTATCGATACTG
1 GGTATCGATACTG
10951 AGTTCACTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 1 0.03
20 24 0.83
21 4 0.14
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (19 bp):
GGTATCGATACTGCAGGGA
Found at i:12763 original size:33 final size:34
Alignment explanation
Indices: 12701--12779 Score: 151
Period size: 34 Copynumber: 2.4 Consensus size: 34
12691 CTGAAGATAG
12701 AAAAATATTGATGACGACCTTTAATAAGTGCTCA
1 AAAAATATTGATGACGACCTTTAATAAGTGCTCA
12735 AAAAATATTGATGACGACCTTTAA-AAGTGCTCA
1 AAAAATATTGATGACGACCTTTAATAAGTGCTCA
12768 AAAAATATTGAT
1 AAAAATATTGAT
12780 TAATGCTGCT
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 21 0.47
34 24 0.53
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.29
Consensus pattern (34 bp):
AAAAATATTGATGACGACCTTTAATAAGTGCTCA
Found at i:15320 original size:29 final size:29
Alignment explanation
Indices: 15287--15346 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
15277 AATGAAAAAG
*
15287 GATAAGTTTGGAA-TATATAATAGTCAAAT
1 GATAAGTTTAGAACT-TATAATAGTCAAAT
* * *
15316 GATAATTTTATAACTTTTAATAGTCAAAT
1 GATAAGTTTAGAACTTATAATAGTCAAAT
15345 GA
1 GA
15347 CTCAACAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
29 25 0.96
30 1 0.04
ACGTcount: A:0.43, C:0.05, G:0.13, T:0.38
Consensus pattern (29 bp):
GATAAGTTTAGAACTTATAATAGTCAAAT
Found at i:16807 original size:2 final size:2
Alignment explanation
Indices: 16764--16788 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16754 TTAATCTATG
16764 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
16789 TTTAAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17034 original size:52 final size:54
Alignment explanation
Indices: 16949--17055 Score: 200
Period size: 52 Copynumber: 2.0 Consensus size: 54
16939 TATTCGCCTG
16949 TCCCACCCCCACCCCCACATTCAAATATTTTCTTATCCTCAAGCAAATCAACTT
1 TCCCACCCCCACCCCCACATTCAAATATTTTCTTATCCTCAAGCAAATCAACTT
17003 TCCCACCCCCA-CCCC-CATTCAAATATTTTCTTATCCTCAAGCAAATCAACTT
1 TCCCACCCCCACCCCCACATTCAAATATTTTCTTATCCTCAAGCAAATCAACTT
17055 T
1 T
17056 AGTATGAAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
52 38 0.72
53 4 0.08
54 11 0.21
ACGTcount: A:0.29, C:0.40, G:0.02, T:0.29
Consensus pattern (54 bp):
TCCCACCCCCACCCCCACATTCAAATATTTTCTTATCCTCAAGCAAATCAACTT
Found at i:20078 original size:28 final size:28
Alignment explanation
Indices: 20038--20094 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
20028 GCTATTGACT
20038 CTTATAAGGCGACAATTTTGGCAAACGC
1 CTTATAAGGCGACAATTTTGGCAAACGC
*
20066 CTTATAAGGCGACAATTTTGGTAAACGC
1 CTTATAAGGCGACAATTTTGGCAAACGC
20094 C
1 C
20095 ACTACCGACG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (28 bp):
CTTATAAGGCGACAATTTTGGCAAACGC
Found at i:21250 original size:27 final size:27
Alignment explanation
Indices: 21220--21276 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
21210 GGTTTTAAAA
* *
21220 ATATATACATTTGAAATTATACTTTAT
1 ATATATACATTTGAAATTATAATATAT
**
21247 ATATATAGTTTTGAAATTATAATATAT
1 ATATATACATTTGAAATTATAATATAT
21274 ATA
1 ATA
21277 GTTTTAAAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (27 bp):
ATATATACATTTGAAATTATAATATAT
Found at i:21271 original size:23 final size:25
Alignment explanation
Indices: 21244--21309 Score: 82
Period size: 23 Copynumber: 2.7 Consensus size: 25
21234 AATTATACTT
*
21244 TATATATATAGTTTTGAAA-TTATA
1 TATATATATAGTTTTGAAACGTATA
*
21268 -ATATATATAGTTTTAAAACGTATA
1 TATATATATAGTTTTGAAACGTATA
*
21292 TATAATATATAATTTTGA
1 TAT-ATATATAGTTTTGA
21310 TAAAAAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
23 17 0.49
24 4 0.11
25 2 0.06
26 12 0.34
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.47
Consensus pattern (25 bp):
TATATATATAGTTTTGAAACGTATA
Found at i:21409 original size:20 final size:21
Alignment explanation
Indices: 21367--21412 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
21357 AAATTATAAC
*
21367 ATATAGTTTTTAAAACGCATAT
1 ATATAATTTTTAAAAC-CATAT
*
21389 ATATAATTTTTAAAA-CTTAT
1 ATATAATTTTTAAAACCATAT
21409 ATAT
1 ATAT
21413 TTTGTCTAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 8 0.36
22 14 0.64
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (21 bp):
ATATAATTTTTAAAACCATAT
Found at i:32923 original size:21 final size:21
Alignment explanation
Indices: 32897--32939 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
32887 ATTGTAATAG
32897 ATGAACCATTTTACTCCTACC
1 ATGAACCATTTTACTCCTACC
32918 ATGAACCATTTTACTCCTACC
1 ATGAACCATTTTACTCCTACC
32939 A
1 A
32940 AAATGTACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.33, G:0.05, T:0.33
Consensus pattern (21 bp):
ATGAACCATTTTACTCCTACC
Found at i:35047 original size:18 final size:17
Alignment explanation
Indices: 35026--35063 Score: 53
Period size: 15 Copynumber: 2.3 Consensus size: 17
35016 TATGTCCCAT
35026 AGGACCACTACGTCCCGA
1 AGGA-CACTACGTCCCGA
35044 AGG--ACTACGTCCCGA
1 AGGACACTACGTCCCGA
35059 AGGAC
1 AGGAC
35064 TACAATACCC
Statistics
Matches: 18, Mismatches: 0, Indels: 5
0.78 0.00 0.22
Matches are distributed among these distances:
15 15 0.83
18 3 0.17
ACGTcount: A:0.29, C:0.34, G:0.26, T:0.11
Consensus pattern (17 bp):
AGGACACTACGTCCCGA
Found at i:35052 original size:15 final size:15
Alignment explanation
Indices: 35032--35066 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
35022 CCATAGGACC
35032 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
35047 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
35062 ACTAC
1 ACTAC
35067 AATACCCTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.29, C:0.34, G:0.23, T:0.14
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:36496 original size:22 final size:23
Alignment explanation
Indices: 36463--36505 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
36453 TCTATAAAAA
*
36463 TACAATCATATAGTT-CTATTAG
1 TACAATCATATACTTACTATTAG
36485 TACAA-CAGTATACTTACTATT
1 TACAATCA-TATACTTACTATT
36506 CCATCAGATC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 2 0.11
22 11 0.61
23 5 0.28
ACGTcount: A:0.37, C:0.16, G:0.07, T:0.40
Consensus pattern (23 bp):
TACAATCATATACTTACTATTAG
Found at i:44914 original size:19 final size:20
Alignment explanation
Indices: 44877--44915 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
44867 TTTTTCCTTT
44877 AGGGGGAATCGATACCCCCC
1 AGGGGGAATCGATACCCCCC
44897 AGGGGGAATCGATACCCCC
1 AGGGGGAATCGATACCCCC
44916 TGGACATTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.33, G:0.31, T:0.10
Consensus pattern (20 bp):
AGGGGGAATCGATACCCCCC
Found at i:48968 original size:35 final size:35
Alignment explanation
Indices: 48923--48990 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
48913 CACCGAAATT
48923 AATTAGCTGACCCTATTCCCATATGTAATGGGGAA
1 AATTAGCTGACCCTATTCCCATATGTAATGGGGAA
48958 AATTAGCTGACCCTATTCCCATATGTAATGGGG
1 AATTAGCTGACCCTATTCCCATATGTAATGGGG
48991 TAAGGGGGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (35 bp):
AATTAGCTGACCCTATTCCCATATGTAATGGGGAA
Found at i:55058 original size:68 final size:70
Alignment explanation
Indices: 54934--55067 Score: 173
Period size: 68 Copynumber: 1.9 Consensus size: 70
54924 TTTACCAACT
* * * * * *
54934 ATCGGTTATTTTAACGTGATAAGACACTAGATTTTTTAAGTAATATTAACGGTTC-AATCTTGAT
1 ATCGGTTATTCTAACATGAT-AGACACTAGATTTTTTAAGCAAGATCAACGATTCAAATCTTGAT
54998 TAAACG
65 TAAACG
**
55004 ATCGGTTATTCTAACATGAT-GACACTAGATTTTTTAAGCAAGATCAGTGATTCAAATCTTGATT
1 ATCGGTTATTCTAACATGATAGACACTAGATTTTTTAAGCAAGATCAACGATTCAAATCTTGATT
55068 TTTGCGTATG
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
68 27 0.49
69 10 0.18
70 18 0.33
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.38
Consensus pattern (70 bp):
ATCGGTTATTCTAACATGATAGACACTAGATTTTTTAAGCAAGATCAACGATTCAAATCTTGATT
AAACG
Found at i:62410 original size:26 final size:27
Alignment explanation
Indices: 62381--62433 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
62371 AGCCTCTCAA
* * *
62381 AATTTCAAAAAA-ATTAGTTAAACCCT
1 AATTTAAAAAAACATAAATTAAACCCT
62407 AATTTAAAAAAACATAAATTAAACCCT
1 AATTTAAAAAAACATAAATTAAACCCT
62434 TCAAAATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.55, C:0.15, G:0.02, T:0.28
Consensus pattern (27 bp):
AATTTAAAAAAACATAAATTAAACCCT
Found at i:67371 original size:19 final size:21
Alignment explanation
Indices: 67344--67386 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
67334 CACTCACTAC
*
67344 TGTATTACTTGCATCGA-TTG
1 TGTATTACTTGCATAGATTTG
67364 TGTA-TACTTGCATAGATTTG
1 TGTATTACTTGCATAGATTTG
67384 TGT
1 TGT
67387 GCCATATCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.21, C:0.12, G:0.21, T:0.47
Consensus pattern (21 bp):
TGTATTACTTGCATAGATTTG
Found at i:73904 original size:15 final size:15
Alignment explanation
Indices: 73880--73927 Score: 51
Period size: 17 Copynumber: 3.0 Consensus size: 15
73870 ATATTCCTTG
73880 TTTTATTTATATATAT
1 TTTTA-TTATATATAT
*
73896 TTTTATTATATATCT
1 TTTTATTATATATAT
*
73911 TATATCATTATATATAT
1 T-T-TTATTATATATAT
73928 ATGTATAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 10 0.37
16 6 0.22
17 11 0.41
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTATTATATATAT
Found at i:74035 original size:5 final size:5
Alignment explanation
Indices: 74027--74079 Score: 54
Period size: 5 Copynumber: 10.4 Consensus size: 5
74017 AATATTCTAT
* * *
74027 TTTTA TTTTA TTATTA TATATA TTATA TTTTA CTTTA TTTTA -TTTA TTTTA
1 TTTTA TTTTA TT-TTA T-TTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
74078 TT
1 TT
74080 ATTTTTTAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
4 4 0.10
5 29 0.71
6 7 0.17
7 1 0.02
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (5 bp):
TTTTA
Found at i:74064 original size:24 final size:22
Alignment explanation
Indices: 74030--74082 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 22
74020 ATTCTATTTT
74030 TATTTTATTATTATATATATTA
1 TATTTTATTATTATATATATTA
* *
74052 TATTTTACT-TTAT-TTTATT-
1 TATTTTATTATTATATATATTA
74071 TATTTTATTATT
1 TATTTTATTATT
74083 TTTTAATATC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 8 0.30
20 7 0.26
21 4 0.15
22 8 0.30
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (22 bp):
TATTTTATTATTATATATATTA
Found at i:74069 original size:17 final size:15
Alignment explanation
Indices: 74024--74087 Score: 57
Period size: 14 Copynumber: 4.6 Consensus size: 15
74014 CTTAATATTC
74024 TATT-TTTATTTTAT
1 TATTATTTATTTTAT
* *
74038 TATTATATATATTA-
1 TATTATTTATTTTAT
*
74052 TA-T-TTTACTTTAT
1 TATTATTTATTTTAT
74065 T-TTATTTATTTTAT
1 TATTATTTATTTTAT
*
74079 TATTTTTTA
1 TATTATTTA
74088 ATATCATGTA
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
12 6 0.16
13 3 0.08
14 16 0.42
15 13 0.34
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.72
Consensus pattern (15 bp):
TATTATTTATTTTAT
Found at i:74069 original size:26 final size:27
Alignment explanation
Indices: 74018--74084 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
74008 TTTTTTCTTA
* *
74018 ATATTCTATTTTTATTTTATTATTATAT
1 ATATTATA-TTTTACTTTATTATTATAT
*
74046 ATATTATATTTTACTTTATT-TTATTT
1 ATATTATATTTTACTTTATTATTATAT
*
74072 ATTTTATTATTTT
1 ATATTA-TATTTT
74085 TTAATATCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
26 10 0.29
27 17 0.50
28 7 0.21
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (27 bp):
ATATTATATTTTACTTTATTATTATAT
Found at i:74217 original size:18 final size:17
Alignment explanation
Indices: 74185--74229 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
74175 TGTACACATT
74185 ATTTTTATT-CCTTTTTA
1 ATTTTT-TTACCTTTTTA
*
74202 ATTTCTTTTACCTTTTTT
1 ATTT-TTTTACCTTTTTA
74220 ATTTTTTTAC
1 ATTTTTTTAC
74230 TCCATTAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.16, C:0.13, G:0.00, T:0.71
Consensus pattern (17 bp):
ATTTTTTTACCTTTTTA
Found at i:74227 original size:17 final size:17
Alignment explanation
Indices: 74183--74229 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
74173 TATGTACACA
74183 TTATTTTTATT-CCTTTT
1 TTATTTTT-TTACCTTTT
*
74200 TAATTTCTTTTACCTTTT
1 TTATTT-TTTTACCTTTT
74218 TTATTTTTTTAC
1 TTATTTTTTTAC
74230 TCCATTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (17 bp):
TTATTTTTTTACCTTTT
Found at i:77397 original size:11 final size:11
Alignment explanation
Indices: 77378--77419 Score: 50
Period size: 10 Copynumber: 3.7 Consensus size: 11
77368 AGATTAAACC
*
77378 AGAACAAAAAG
1 AGAAAAAAAAG
77389 AG-AAAAAAAG
1 AGAAAAAAAAG
77399 AGAAAATAAAAAG
1 AG-AAA-AAAAAG
77412 AGAAAAAA
1 AGAAAAAA
77420 CAAAGGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
10 9 0.33
11 5 0.19
12 5 0.19
13 8 0.30
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (11 bp):
AGAAAAAAAAG
Found at i:77411 original size:13 final size:13
Alignment explanation
Indices: 77393--77430 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
77383 AAAAAGAGAA
77393 AAAAAGAGAAAAT
1 AAAAAGAGAAAAT
77406 AAAAAGAGAAAA-
1 AAAAAGAGAAAAT
77418 AACAAAG-GAAAAT
1 AA-AAAGAGAAAAT
77431 TGAAGAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.30
13 16 0.70
ACGTcount: A:0.76, C:0.03, G:0.16, T:0.05
Consensus pattern (13 bp):
AAAAAGAGAAAAT
Found at i:77428 original size:25 final size:23
Alignment explanation
Indices: 77383--77430 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
77373 AAACCAGAAC
*
77383 AAAAAGAGAAAAAAAGAGAAAAT
1 AAAAAGAGAAAAAAAAAGAAAAT
77406 AAAAAGAGAAAAAACAAAGGAAAAT
1 AAAAAGAGAAAAAA-AAA-GAAAAT
77431 TGAAGAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 14 0.64
24 2 0.09
25 6 0.27
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.04
Consensus pattern (23 bp):
AAAAAGAGAAAAAAAAAGAAAAT
Found at i:77618 original size:69 final size:69
Alignment explanation
Indices: 77500--77637 Score: 249
Period size: 69 Copynumber: 2.0 Consensus size: 69
77490 GATTCAAACT
*
77500 ATGAGATTGATCAAGCACAATCATTTCTGAATCACTGAACCACTTCACTCGAAGATCATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTCTGAATCACTGAACCACTCCACTCGAAGATCATAGAGCA
77565 TCAA
66 TCAA
* *
77569 ATGAGATTTATCAAGCACAATCATTTCTGAATCACTGAATCACTCCACTCGAAGATCATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTCTGAATCACTGAACCACTCCACTCGAAGATCATAGAGCA
77634 TCAA
66 TCAA
77638 GAGAGAGACA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (69 bp):
ATGAGATTGATCAAGCACAATCATTTCTGAATCACTGAACCACTCCACTCGAAGATCATAGAGCA
TCAA
Found at i:79070 original size:35 final size:36
Alignment explanation
Indices: 79024--79110 Score: 140
Period size: 36 Copynumber: 2.4 Consensus size: 36
79014 ATTGAAAACA
* *
79024 TTTCCCTTGAAACGAATTT-TTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGATAG
*
79059 TTTCCCATGAAACAAATTTCGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGATAG
79095 TTTCCCTTGAAACAAA
1 TTTCCCTTGAAACAAA
79111 ATCTTTGAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
35 17 0.36
36 30 0.64
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.38
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGATAG
Found at i:79127 original size:100 final size:99
Alignment explanation
Indices: 78939--79162 Score: 272
Period size: 100 Copynumber: 2.2 Consensus size: 99
78929 TAAAAAGAAG
* * * *
78939 ATTTATCTCCTTGAGATAGTTTCCCTTGAAACAAAATTTGGTCTCCCTTGAGACAGTTTCTCTTG
1 ATTTTTCTCCTTGAGATAGTTTCCCATGAAACAAAATTTCGTCTCCCTTGAGACAGTTTCCCTTG
* *
79004 AAACATAAACATTGAAAACATTTCCCTTGAAACGA
66 AAACATAAACATTGAAAACATTTCCC-TAAAACAA
* *
79039 ATTTTTCTCTCTTGAGATAGTTTCCCATGAAAC-AAATTTCGTCTCTCTTGAGATAGTTTCCCTT
1 ATTTTTCTC-CTTGAGATAGTTTCCCATGAAACAAAATTTCGTCTCCCTTGAGACAGTTTCCCTT
* ***
79103 GAAACA-AAATCTTTGAATTTATTTCCCTAAAACAA
65 GAAACATAAA-CATTGAAAACATTTCCCTAAAACAA
*
79138 ATTTTGTCTCACTTGAGACAGTTTC
1 ATTTT-TCTC-CTTGAGATAGTTTC
79163 TTGAAACACA
Statistics
Matches: 107, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
99 14 0.13
100 71 0.66
101 22 0.21
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.38
Consensus pattern (99 bp):
ATTTTTCTCCTTGAGATAGTTTCCCATGAAACAAAATTTCGTCTCCCTTGAGACAGTTTCCCTTG
AAACATAAACATTGAAAACATTTCCCTAAAACAA
Found at i:79174 original size:64 final size:64
Alignment explanation
Indices: 79059--79251 Score: 194
Period size: 64 Copynumber: 2.9 Consensus size: 64
79049 CTTGAGATAG
* * *
79059 TTTCCCATGAAACAAATTTCGTCTCTCTTGAGATAGTTTCCCTTG-AA-ACAAAATCTTTGAATT
1 TTTCCCATAAAACAAATTTTGTCTC-CTTGAGACAGTTT--CTTGAAACACAAAATCTTTGAATT
79122 TA
63 TA
**
79124 TTTCCC-TAAAACAAATTTTGTCTCACTTGAGACAGTTTCTTGAAACACAAAATCTTCAAATTTA
1 TTTCCCATAAAACAAATTTTGTCTC-CTTGAGACAGTTTCTTGAAACACAAAATCTTTGAATTTA
* * * * *
79188 TTTCCCTTAAAACAAAATTTTGTTTTCCTTGAGACCGTTTTCATGAAACAACATATATCTTTGA
1 TTTCCCATAAAAC-AAATTTTG-TCTCCTTGAGACAG-TTTCTTGAAAC-ACA-AAATCTTTGA
79252 GATCGTTTTC
Statistics
Matches: 108, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
62 4 0.04
63 2 0.02
64 50 0.46
65 12 0.11
66 17 0.16
67 13 0.12
68 3 0.03
69 7 0.06
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.38
Consensus pattern (64 bp):
TTTCCCATAAAACAAATTTTGTCTCCTTGAGACAGTTTCTTGAAACACAAAATCTTTGAATTTA
Found at i:80191 original size:104 final size:105
Alignment explanation
Indices: 79938--80207 Score: 300
Period size: 109 Copynumber: 2.5 Consensus size: 105
79928 ACGAAGGGGC
* * *
79938 TTCCCAGTTTTAGAGCCAATTTCAACTTCACA-GTGAGTGATATTGGACTCAAGACAACACAAGC
1 TTCCCAGTTTCAGAGCCAATTTCAACTTCACACG-GAG-GATATTGGACTCGAGACAACACAAAC
* *
80002 TCAACTTCACAACGAATGGGGACTGATTGTCAACAAACAACT
64 TCAACTTCACAACGAATGGGGACTGACTATCAACAAACAACT
* * * *
80044 TT-TCAGTTTTATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGAACTCGAGACAACACA
1 TTCCCAG---T-TTCAGAGCCAATTTCAACTTCACA-CGGAGGATATTGGACTCGAGACAACACA
*
80108 AACTCAACTTCACAGCGAA-GGGG-CGGTG-CTATCAACAAACAA-T
61 AACTCAACTTCACAACGAATGGGGAC--TGACTATCAACAAACAACT
* *
80151 TTCCCAGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGGACTCGAAACAA
1 TTCCCAGTTTCAGAGCCAATTTCAACTTCAC-ACGGAGGATATTGGACTCGAGACAA
80208 TACTACCCAC
Statistics
Matches: 138, Mismatches: 16, Indels: 22
0.78 0.09 0.12
Matches are distributed among these distances:
104 42 0.30
105 5 0.04
106 2 0.01
107 4 0.03
108 20 0.14
109 62 0.45
110 2 0.01
111 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (105 bp):
TTCCCAGTTTCAGAGCCAATTTCAACTTCACACGGAGGATATTGGACTCGAGACAACACAAACTC
AACTTCACAACGAATGGGGACTGACTATCAACAAACAACT
Found at i:81523 original size:16 final size:16
Alignment explanation
Indices: 81498--81570 Score: 56
Period size: 16 Copynumber: 4.3 Consensus size: 16
81488 TCGTCCCCTA
* *
81498 TATATATTTTTTTAAT
1 TATATTTTTTTTTATT
*
81514 TATATTTTTTATTATT
1 TATATTTTTTTTTATT
81530 TACTATATTCCTTTTTTATT
1 TA-TAT-TT--TTTTTTATT
* * *
81550 TATATTATTATTTATA
1 TATATTTTTTTTTATT
81566 TATAT
1 TATAT
81571 ATCTATATCA
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
16 27 0.59
17 3 0.07
18 3 0.07
19 3 0.07
20 10 0.22
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (16 bp):
TATATTTTTTTTTATT
Found at i:81578 original size:41 final size:36
Alignment explanation
Indices: 81505--81572 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
81495 CTATATATAT
*
81505 TTTTTTAATTATATTTTTTATTATTTACTATATTCC
1 TTTTTTAATTATATTTTTTATTATATACTATATTCC
* *
81541 TTTTTTATTTATA-TTATTATTTATATA-TATAT
1 TTTTTTAATTATATTTTTTA-TTATATACTATAT
81573 CTATATCATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
35 10 0.36
36 18 0.64
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (36 bp):
TTTTTTAATTATATTTTTTATTATATACTATATTCC
Found at i:81651 original size:17 final size:17
Alignment explanation
Indices: 81629--81689 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
81619 ACTATGTATA
81629 ATATTTTTCTTAATATT
1 ATATTTTTCTTAATATT
**
81646 ATATTTTTACGTTTTTA-T
1 ATATTTTT-C-TTAATATT
81664 ATATATTTTCTTAATATT
1 ATAT-TTTTCTTAATATT
*
81682 CTATTTTT
1 ATATTTTT
81690 GTTTCTATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
17 16 0.46
18 11 0.31
19 8 0.23
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.66
Consensus pattern (17 bp):
ATATTTTTCTTAATATT
Found at i:81954 original size:9 final size:8
Alignment explanation
Indices: 81934--81984 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 8
81924 TTTTTTAACA
81934 TTTTA-TT
1 TTTTATTT
81941 TTTTATTT
1 TTTTATTT
81949 TGTTTATTT
1 T-TTTATTT
81958 TTATTA-TT
1 TT-TTATTT
81966 TTTTAGTTT
1 TTTTA-TTT
*
81975 TGTTATTT
1 TTTTATTT
81983 TT
1 TT
81985 CATTTTTTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
7 8 0.22
8 12 0.32
9 17 0.46
ACGTcount: A:0.14, C:0.00, G:0.06, T:0.80
Consensus pattern (8 bp):
TTTTATTT
Found at i:81970 original size:25 final size:26
Alignment explanation
Indices: 81936--81992 Score: 84
Period size: 25 Copynumber: 2.3 Consensus size: 26
81926 TTTTAACATT
81936 TTATTTTTTA-TTTTGTTTATTTTT-A
1 TTATTTTTTAGTTTTG-TTATTTTTCA
81961 TTATTTTTTAGTTTTGTTATTTTTCA
1 TTATTTTTTAGTTTTGTTATTTTTCA
81987 TT-TTTT
1 TTATTTT
81993 CTTTTTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
25 22 0.73
26 8 0.27
ACGTcount: A:0.14, C:0.02, G:0.05, T:0.79
Consensus pattern (26 bp):
TTATTTTTTAGTTTTGTTATTTTTCA
Found at i:81984 original size:16 final size:14
Alignment explanation
Indices: 81934--81998 Score: 58
Period size: 16 Copynumber: 4.2 Consensus size: 14
81924 TTTTTTAACA
81934 TTTTATTTTTTATTT
1 TTTTATTTTTTA-TT
81949 TGTTTATTTTTATTATT
1 T-TTTA-TTTT-TTATT
81966 TTTTAGTTTTGTTATT
1 TTTTA-TTTT-TTATT
* *
81982 TTTCATTTTTTCTT
1 TTTTATTTTTTATT
81996 TTT
1 TTT
81999 ATTATTCTCA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
14 7 0.16
15 5 0.12
16 21 0.49
17 7 0.16
18 3 0.07
ACGTcount: A:0.12, C:0.03, G:0.05, T:0.80
Consensus pattern (14 bp):
TTTTATTTTTTATT
Done.